# HG changeset patch
# User iuc
# Date 1572610348 14400
# Node ID 284bb0c05da929cb48fdc8b4f5e5beda1946a469
# Parent  dc0f01791c9bf2502a6282f360931d55eb02718d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 3b8670ad0ce9dd90d6a24429bca131362e56d17d"

diff -r dc0f01791c9b -r 284bb0c05da9 analyze_diff_expr.xml
--- a/analyze_diff_expr.xml	Fri Apr 26 06:45:46 2019 -0400
+++ b/analyze_diff_expr.xml	Fri Nov 01 08:12:28 2019 -0400
@@ -4,10 +4,10 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="2.10.0">bioconductor-qvalue</requirement>
-        <requirement type="package" version="1.30.0">bioconductor-goseq</requirement>
-        <requirement type="package" version="2.0.6">r-cluster</requirement>
-        <requirement type="package" version="1.1.24">r-fastcluster</requirement>
+        <requirement type="package" version="2.16.0">bioconductor-qvalue</requirement>
+        <requirement type="package" version="1.36.0">bioconductor-goseq</requirement>
+        <requirement type="package" version="2.0.8">r-cluster</requirement>
+        <requirement type="package" version="1.1.25">r-fastcluster</requirement>
     </expand>
     <command detect_errors="aggressive"><![CDATA[
     ## DE results input files must be in the working directory and have suffix .DE_results
diff -r dc0f01791c9b -r 284bb0c05da9 macros.xml
--- a/macros.xml	Fri Apr 26 06:45:46 2019 -0400
+++ b/macros.xml	Fri Nov 01 08:12:28 2019 -0400
@@ -7,7 +7,7 @@
         </requirements>
     </xml>
 
-    <token name="@WRAPPER_VERSION@">2.8.4</token>
+    <token name="@WRAPPER_VERSION@">2.8.5</token>
 
     <token name="@COMMAND_PAIRED_STRAND_JACCARD@">
         #if $pool.inputs.strand.is_strand_specific:
diff -r dc0f01791c9b -r 284bb0c05da9 test-data/count/contig_exn50_statistic/ExN50.stats
--- a/test-data/count/contig_exn50_statistic/ExN50.stats	Fri Apr 26 06:45:46 2019 -0400
+++ b/test-data/count/contig_exn50_statistic/ExN50.stats	Fri Nov 01 08:12:28 2019 -0400
@@ -1,4 +1,5 @@
 Ex	ExN50	num_transcripts
 33	541	1
 67	541	2
+99	380	3
 100	279	7
diff -r dc0f01791c9b -r 284bb0c05da9 test-data/supertranscripts/trinity_genes.fasta
--- a/test-data/supertranscripts/trinity_genes.fasta	Fri Apr 26 06:45:46 2019 -0400
+++ b/test-data/supertranscripts/trinity_genes.fasta	Fri Nov 01 08:12:28 2019 -0400
@@ -1,14 +1,14 @@
->TRINITY_DN1_c0_g1
-CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATGTATATGGTACAGATGTAAAG
+>TRINITY_DN2_c3_g1
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACCAA
 >TRINITY_DN0_c0_g1
 AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
 >TRINITY_DN2_c0_g1
 TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
->TRINITY_DN2_c1_g1
-GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTG
+>TRINITY_DN3_c0_g1
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
 >TRINITY_DN2_c2_g1
 ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGAGTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGCTACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
->TRINITY_DN2_c3_g1
-GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACCAA
->TRINITY_DN3_c0_g1
-ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
+>TRINITY_DN2_c1_g1
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTG
+>TRINITY_DN1_c0_g1
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATGTATATGGTACAGATGTAAAG
diff -r dc0f01791c9b -r 284bb0c05da9 test-data/supertranscripts/trinity_genes.gtf
--- a/test-data/supertranscripts/trinity_genes.gtf	Fri Apr 26 06:45:46 2019 -0400
+++ b/test-data/supertranscripts/trinity_genes.gtf	Fri Nov 01 08:12:28 2019 -0400
@@ -1,14 +1,14 @@
-TRINITY_DN1_c0_g1	Trinity_gene	exon	1	380	.	+	.	gene_id "TRINITY_DN1_c0_g1"; transcript_id "TRINITY_DN1_c0_g1_i1"
+TRINITY_DN2_c3_g1	Trinity_gene	exon	1	202	.	+	.	gene_id "TRINITY_DN2_c3_g1"; transcript_id "TRINITY_DN2_c3_g1_i1"
 
 TRINITY_DN0_c0_g1	Trinity_gene	exon	1	229	.	+	.	gene_id "TRINITY_DN0_c0_g1"; transcript_id "TRINITY_DN0_c0_g1_i1"
 
 TRINITY_DN2_c0_g1	Trinity_gene	exon	1	279	.	+	.	gene_id "TRINITY_DN2_c0_g1"; transcript_id "TRINITY_DN2_c0_g1_i1"
 
-TRINITY_DN2_c1_g1	Trinity_gene	exon	1	541	.	+	.	gene_id "TRINITY_DN2_c1_g1"; transcript_id "TRINITY_DN2_c1_g1_i1"
+TRINITY_DN3_c0_g1	Trinity_gene	exon	1	216	.	+	.	gene_id "TRINITY_DN3_c0_g1"; transcript_id "TRINITY_DN3_c0_g1_i1"
 
 TRINITY_DN2_c2_g1	Trinity_gene	exon	1	240	.	+	.	gene_id "TRINITY_DN2_c2_g1"; transcript_id "TRINITY_DN2_c2_g1_i1"
 
-TRINITY_DN2_c3_g1	Trinity_gene	exon	1	202	.	+	.	gene_id "TRINITY_DN2_c3_g1"; transcript_id "TRINITY_DN2_c3_g1_i1"
+TRINITY_DN2_c1_g1	Trinity_gene	exon	1	541	.	+	.	gene_id "TRINITY_DN2_c1_g1"; transcript_id "TRINITY_DN2_c1_g1_i1"
 
-TRINITY_DN3_c0_g1	Trinity_gene	exon	1	216	.	+	.	gene_id "TRINITY_DN3_c0_g1"; transcript_id "TRINITY_DN3_c0_g1_i1"
+TRINITY_DN1_c0_g1	Trinity_gene	exon	1	380	.	+	.	gene_id "TRINITY_DN1_c0_g1"; transcript_id "TRINITY_DN1_c0_g1_i1"